The present study aimed at systematically investigating the endophytic communities of dominant plants in the karst ecosystem. Soil and plant materials were collected and after sequencing of the 16 s RNA, the diversity and abundance of the endophytic community structures in leaves were examined. Our results showed that abundant and diverse endogenous bacteria were associated with the leaves of common dominant plants living in the karst ecological environment. Notably, common traits and significant differences in the endophytic community structures were recorded among different plant species with different leaf grown in soils with different calcium contents. These observations implied that plants may adopt different strategies to adapt to the karst ecological environment. In addition, the endophytic bacteria associated with the leaves may be involved in different physiological strategies used by the plants to adapt to the karst ecological environment. These findings provide new avenues for developing microbial agents that could be suitable for the karst ecological environment and will provide sustainable solutions for improving the ability of plants to adapt to karst special adversities, and thus for karst geomorphological environmental protection and agricultural development.